Contacts of the helix formed by residues 45 - 57 (chain J) in PDB entry 3Q2K
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 45 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43J ASP* 2.7 13.6 + - - +
44J THR* 1.3 79.4 + - - +
46J PRO* 1.3 69.3 - - - +
47J GLU* 3.5 15.6 + - - +
48J ALA* 2.6 42.6 + - + +
49J LEU* 3.0 16.8 + - - +
500J NAI 3.6 13.0 - - - +
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Residues in contact with PRO 46 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43J ASP 5.0 0.4 - - - +
44J THR 3.2 11.2 - - - +
45J ASN* 1.3 85.8 - - + +
47J GLU* 1.3 57.7 + - + +
49J LEU* 2.9 13.4 + - + +
50J GLN* 2.7 52.2 + - + +
62J SER* 6.2 3.1 - - - -
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Residues in contact with GLU 47 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45J ASN* 3.4 14.3 + - - +
46J PRO* 1.3 85.3 - - + +
48J ALA* 1.3 58.6 + - - +
50J GLN* 3.4 18.9 + - - +
51J ALA* 3.0 28.8 + - - +
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Residues in contact with ALA 48 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J CYS* 3.8 15.4 - - - +
19J GLY* 5.6 0.2 - - - -
43J ASP* 3.7 20.6 - - - +
45J ASN* 2.6 25.4 + - - +
47J GLU* 1.3 73.6 - - - +
49J LEU* 1.3 58.0 + - - +
51J ALA* 3.6 6.1 + - - +
52J ALA* 3.1 27.4 + - - +
500J NAI 3.8 8.7 - - - +
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Residues in contact with LEU 49 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J CYS* 4.9 1.3 - - - -
41J ILE* 3.9 21.5 - - + +
42J CYS* 4.2 1.6 - - - -
43J ASP* 3.4 36.3 - - + +
45J ASN 3.0 4.5 + - - +
46J PRO* 2.9 11.7 + - + +
48J ALA* 1.3 77.4 - - - +
50J GLN* 1.3 64.8 + - - +
52J ALA* 3.3 3.2 + - - +
53J GLU* 3.1 22.2 + - - +
60J PRO* 3.9 27.6 - - + -
61J PHE 3.5 31.9 - - - +
62J SER* 4.0 9.9 - - - -
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Residues in contact with GLN 50 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46J PRO* 2.7 36.6 + - + +
47J GLU* 3.6 21.7 - - - +
49J LEU* 1.3 76.6 - - + +
51J ALA* 1.3 62.1 + - - +
53J GLU* 3.2 17.8 + - - +
54J ALA* 3.2 14.8 + - - +
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Residues in contact with ALA 51 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47J GLU 3.0 17.5 + - - +
48J ALA* 4.0 6.5 - - - +
50J GLN* 1.3 75.5 - - - +
52J ALA* 1.3 59.9 + - - +
54J ALA* 3.8 7.1 + - - +
55J ALA* 3.5 21.8 + - - +
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Residues in contact with ALA 52 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J CYS* 3.3 38.8 - - + -
26J ILE* 5.6 8.5 - - + -
41J ILE* 3.4 9.2 - - + -
48J ALA 3.1 13.2 + - - +
49J LEU 3.8 2.0 - - - +
50J GLN 3.2 0.2 - - - -
51J ALA* 1.3 76.9 - - - +
53J GLU* 1.3 57.3 + - - +
54J ALA 3.1 1.6 - - - -
55J ALA* 3.3 2.9 + - - +
56J THR* 2.2 38.6 + - - +
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Residues in contact with GLU 53 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41J ILE* 3.3 16.3 - - + +
49J LEU 3.1 12.7 + - - +
50J GLN* 3.7 11.6 - - - +
52J ALA* 1.3 78.4 - - - +
54J ALA* 1.3 59.4 + - + +
56J THR* 3.7 1.3 - - - -
57J GLY* 2.5 39.0 + - - +
58J ALA 4.1 8.4 - - - +
60J PRO* 2.8 35.0 - - + +
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Residues in contact with ALA 54 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50J GLN 3.2 12.9 + - - +
51J ALA* 4.2 7.6 - - - +
52J ALA 3.1 0.6 - - - -
53J GLU* 1.3 82.4 - - + +
55J ALA* 1.3 59.7 + - - +
56J THR 3.4 0.2 - - - -
57J GLY* 4.4 0.8 + - - -
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Residues in contact with ALA 55 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J ILE* 5.3 5.8 - - + +
51J ALA 3.5 15.1 + - - +
52J ALA* 3.3 5.4 + - - +
53J GLU 3.2 0.2 - - - -
54J ALA* 1.3 79.3 - - - +
56J THR* 1.3 66.8 + - + +
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Residues in contact with THR 56 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J ILE* 3.8 29.8 - - + -
38J LEU* 3.2 36.7 - - + +
41J ILE* 3.7 8.8 - - + +
52J ALA* 2.2 31.8 + - + +
53J GLU* 3.7 1.0 - - - -
55J ALA* 1.3 87.4 - - + +
57J GLY* 1.3 56.0 + - - +
58J ALA* 3.1 15.5 + - - +
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Residues in contact with GLY 57 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53J GLU* 2.5 29.4 + - - +
54J ALA 4.4 1.2 - - - -
55J ALA 3.9 0.4 - - - -
56J THR* 1.3 71.5 - - - +
58J ALA* 1.3 64.2 + - - +
60J PRO* 5.2 0.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il